Funny noise coming out of speakers...

I have a sproggy DC-DC power supply and it is grounded to the car's chassis in the trunk in my homemade wooden case. When I turn my windows software volume up to max, and turn up my stereo to max, I can hear a sound coming from my speakers which sounds like someone blowing bubbles in water. Kinda like a "glug glug glug glug glug" sound. When I turn the engine off, it continues for about 10 more seconds and then quits. Any idea what this might be? I really don't think I should have noise on my system when I'm using a DC-DC power supply which is grounded to the car's chassis. Additionally when the car is running, I have lots of alternator whine at the highest volumes as well.

Ooops...I should have specified that. I'm using an AUX-in on my pioneer deck. Also I've found the glugging noise is only occuring after driving for awhile. Is it possible my ground wire is too small? It's about 16 gauge coming out of the power supply. The power wire going in, on the other hand, is 8 gauge or so.

Be sure to use shielded RCA cables, and that they don't run along-side any of the power cables. You may also try a ground loop isolator (available at Radio Shack) to solve the alternator whine. I would thing 16 guage wire should be enough to properly ground the PSU.

When you say that you have 16 gauge wire for the ground..is this your negative wire as well? Ideally you should use the same size wire for the positive and ground, as they are as important as one enougher. No point having a huge wire for the power to get into the supply, if you only have a small one comming out.
I'd run 8 gauge all around.

Are you the guy that coudnt find a place to ground to in the trunk and were using a screw? Use a bolt and nut with one of those star grounding washers (or just scrape the hell out of the paint on your car, i like the grounding washer better).

Also, the quality of the wire makes a difference (i think). I had all kinds of noise caused by a bad ground. I connected a wire to chassis ground and went around the car touching all the components with it (amps, inverter, case). When i touched the case the noise went away. I dont know if it was the fact that the wire was some chepe no name stuff or the fact that grounding case was its 10th use since i owned it i dont know, but grounds can be a *****.

As for the bubbling sound, never heard that one before. Start isolating components so you can find where the noise is entering the system. A good way is to cut an old set of rca wires in half and ground the center conductor to the outside jacket and connect that to the inputs of your amps, headunit etc. This makes sure the input is grounded and no noise is comming in there. Just dont connect that cable to the output of anything for obvious reasons.